VIOLIN: Vaccine Investigation and Online Information Network

Publications

Search for PubMed for Dr. Yongqun "Oliver" He's vaccine or ontology related publications between 2008 and 2022:

Vaccine related: https://www.ncbi.nlm.nih.gov/pubmed/?term=(yongqun+he)+AND+vaccine+AND+2008%3A2022%5Bdp%5D&sort=date
Vaccine or Ontology related: https://www.ncbi.nlm.nih.gov/pubmed/?term=(yongqun+he)+AND+(vaccine+OR+ontology)+AND+2008%3A2022%5Bdp%5D&sort=date

Since 2020, we have performed active COVID-19 related studies, esp. in the area of COVID-19 vaccine research:

COVID-19 related: https://www.ncbi.nlm.nih.gov/pubmed/?term=(yongqun+he)+AND+COVID-19+AND+2020%3A2022%5Bdp%5D&sort=date
COVID-19 vaccine related: https://www.ncbi.nlm.nih.gov/pubmed/?term=(yongqun+he)+AND+vaccine+AND+COVID-19+AND+2020%3A2022%5Bdp%5D&sort=date

Search online for hits citing the grant 1R01AI081062 that supports this VIOLIN and Vaccine Ontology (VO) project:

PubMed : https://www.ncbi.nlm.nih.gov/pubmed/?term=AI081062%5BGr%5D.
Google: https://www.google.com/search?q=1R01AI081062+OR+AI081062.

The following is a list of papers based on different categories (Note: one paper may appears in more than one category; Also, this list may not always updated):

The VIOLIN system in general:

He Y, Racz R, Sayers S, Lin Y, Todd T, Hur J, Li X, Patel M, Zhao B, Chung M, Ostrow J, Sylora A, Dungarani P, Ulysse G, Kochhar K, Vidri B, Strait K, Jourdian GW, Xiang Z. Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Research. 2014. 42 (D1): D1124-D1132. doi: 10.1093/nar/gkt1133. [NAR] [PubMed PMID: 24259431] [PDF]
Xiang Z, Todd T, Ku KP, Kovacic BL, Larson CB, Chen F, Hodges AP, Tian Y, Olenzek EA, Zhao B, Colby LA, Rush HG, Gilsdorf JR, Jourdian GW, He Y. VIOLIN: Vaccine Investigation and Online Information Network. Nucleic Acids Res. 2008 Jan;36(Database issue):D923-8. [NAR] [PubMed: PMID: 1802504] [PDF].

Vaccine design tool Vaxign and newly developed Vaxign-ML:

Papers introducting Vaxign and Vaxign2:

Ong E, Cooke MF, Huffman A, Xiang Z, Wong MU, Wang H, Seetharaman M, Valdez N, He Y. Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. Nucleic Acid Research. 2021. gkab279. https://doi.org/10.1093/nar/gkab279. Published on May 1, 2021.
He Y, Xiang Z, Mobley HLT. Vaxign: the first web-based vaccine design program for reverse vaccinology and an application for vaccine development.J Biomed Biotechnol. 2010;2010:297505. Epub 2010 Jul 4. [PMID:20671958] [Journal Link]
Xiang Z, He Y. Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. BMC Bioinformatics. 2013, 14(Suppl 4):S2 (8 March 2013). PMID: 23514126; PMCID: PMC3599071.
Xiang Z, He Y. 2009. Vaxign: a web-based vaccine target design program for reverse vaccinology. Procedia in Vaccinology. Volume 1, Issue 1, Pages 23-29.
He Y. Genome-based computational vaccine discovery by reverse vaccinology (Chapter 5); in book: Immunomic Discovery of Adjuvants and Candidate Subunit Vaccines, edited by Darren R. Flower, Yvonne Perrie. Publisher: Springer, New York, 2013. ISBN-13: 978-1461450696. ISBN 978-1-4614-5070-2 (eBook). Links in: Google eBook, and Amazon book.

Vaxign Machine Learning (new in 2020):

Ong E, Wang H, Wong MU, Seetharaman M, Valdez N, He Y. Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens. Bioinformatics. Feb 25. pii: btaa119. doi: 10.1093/bioinformatics/btaa119. [Epub ahead of print] (Acceptance date: 2020-02-18). PMID: 32096826.

Selected papers citing Vaxign:

Based on Google Scholars search, Vaxign has been cited for over 260 times as of March 14, 2020, and 346 times as of February 18, 2021.

Below is a list of papers that reported the applications of Vaxign with our own participation:

Haihe Wang, Edison Ong, John Y Kao, Duxin Sun, Yongqun He. Reverse Microbiomics: a new reverse dysbiosis analysis strategy and its usage in prediction of autoantigens and virulent factors in dysbiotic gut microbiomes from rheumatoid arthritis patients. Front. Microbiol. | doi: 10.3389/fmicb.2021.633732. Accepted on Feb 8, 2021.
Ong E, Huang X, Pearce R, Zhang Y, He Y. Computational Design of SARS-CoV-2 Spike Glycoproteins to Increase Immunogenicity by T Cell Epitope Engineering. Comput Struct Biotechnol J. 2021;19:518-529. doi: 10.1016/j.csbj.2020.12.039. Epub 2020 Dec 31. PMID: 33398234. PMCID: PMC7773544.
Ong E, Wong M, Huffman A, He Y. COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning. Frontiers in Immunology. 11:1581. doi: 10.3389/fimmu.2020.01581. (Published: 03 July 2020.) PMID: 32719684. PMCID: PMC7350702.
- note:This is a highly viewed and cited paper related to COVID-19 vaccine design. As of May 25, 2021, this article had more views than 97% of all Frontiers articles (based on the journal statistics), and this article had been cited by 122 publications (based on Google Scholar).
Wang Y, Wen Z, Pan X, Briles DE, He Y, Zhang JR. Novel immunoprotective proteins of Streptococcus pneumoniae identified by opsonophagocytosis killing screen. Infect Immun. 2018 Jun 11. pii: IAI.00423-18. PMID: 29891544.
Lopera-Madrid J, Osorio JE, He Y, Xiang Z, Adams LG, Laughlin RC, Mwangi W, Subramanya S, Neilan J, Brake D, Burrage TG, Brown WC, Clavijo A, Bounpheng MA. Safety and immunogenicity of mammalian cell derived and modified-vaccinia Ankara vectored African swine fever subunit antigens in swine. Veterinary Immunology and Immunopathology. 2017. DOI: 10.1016/j.vetimm.2017.01.004. PMID: 28241999.
Ni Z, Chen Y, Ong E, He Y. Antibiotic resistance determinants-focused Acinetobacter baumannii vaccine design using reverse vaccinology. International Journal of Molecular Sciences. 2017, 18(2), 458. PMID: 28230771. PMCID: PMC5343991.
McNamara L, He Y, Yang Z. Using epitope predictions to evaluate efficacy and population coverage of the Mtb72f vaccine for tuberculosis. BMC Immunology. 2010 Mar 30;11(1):18. [PMID: 20353587] [Journal Link]
He Y, Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Res. 2010 Sep 27;6 Suppl 1:S5. [NAR] [PubMed] [PDF].

Vaccine Components:

Cov19VaxKB: COVID-19 vaccine knowledgebase:

Philip C. Huang, Rohit Goru, Anthony Huffman, Asiyah Yu Lin, Michael F. Cooked, Yongqun He. Cov19VaxKB: A Web-based Integrative COVID-19 Vaccine Knowledge Base. Vaccine: X. Volume 10, April 2022, 100139. PMID: 34981039. PMCID: PMC8716025.

Protegen: Protective Antigens:

Yang B, Sayers S, Xiang Z, He Y. Protegen: a web-based protective antigen database and analysis system. Nucleic Acids Research. 2010. 2010 Oct 19. [Epub ahead of print]. [PMID: 20959289]

Protegen data analysis:

Ong E, Wong MU, He Y. Identification of new features from known bacterial protective vaccine antigens enhances rational vaccine design. Frontiers in Immunology. 2017 Oct 26;8:1382. PMID: 29123525.
He Y, Xiang Z. Bioinformatics analysis of bacterial protective antigens in manually curated Protegen database. Procedia in Vaccinology. 2012. Volume 6. Pages 3 – 9.

Vaxjo: Vaccine Adjuvants:

Sayers S, Ulysse G, Xiang Z, and He Y. Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development.Journal of Biomedicine and Biotechnology. 2012;2012:831486. Epub 2012 Mar 13. PMID: 22505817.

Virmugen: Virulence factors whose mutants are live attenuated vaccines:

Racz R, Chung M, Xiang Z, and He Y. Systematic annotation and analysis of “virmugens” - virulence factors whose mutants can be used as live attenuated vaccines. Vaccine. Available online December 6, 2012. DOI: 10.1016/j.vaccine.2012.11.066.

DNAVaxDB: DNA Vaccine database:

Racz R, Li X, Patel M, Xiang Z, and He Y. DNAVaxDB: the first web-based DNA vaccine database and its data analysis. BMC Bioinformatics. 2014, 15(Suppl 4):S2 (19 March 2014). doi:10.1186/1471-2105-15-S4-S2.

Vaxvec: Recombinant Vaccine Vector database:

Deng S, Martin C, Patil R, Zhu F, Zhao B, Xiang Z, He Y. Vaxvec: The first web-based recombinant vaccine vector database and its data analysis. Vaccine. 2015 Sep 21. pii: S0264-410X(15)01284-0. doi: 10.1016/j.vaccine.2015.07.113. [Epub ahead of print] PMID: 26403370.

Vaccine immune responses:

VaximmutorDB: Vaccine immune factor (which is coined as "vaximmutor") database:

Kimberly Berke, Peter Sun, Edison Ong, Nasim Sanati, Anthony Huffman, Timothy Brunson, Fred Loney, Joseph Ostrow, Rebecca Racz, Bin Zhao, Zuoshuang Xiang, Anna Maria Masci, Jie Zheng, Guanming Wu, Yongqun He, VaximmutorDB: A web-based vaccine immune factor database and its data analysis for understanding vaccine-induced immune responses. Front. Immunol. | doi: 10.3389/fimmu.2021.639491. Accepted on Feb 18, 2021.

Vaxar: Vaccine Animal Responses:

Todd T*, Dunn N*, Xiang Z, He Y. Vaxar: A web-based database of laboratory animal responses to vaccinations and its application in the meta-analysis of different animal responses to tuberculosis vaccinations. Comparative Medicine. 2016. 66(2):119-28. PMID: 27053566.

Ontology development:

VO: Vaccine Ontology:

He Y, Cowell L, Diehl AD, Mobley HL, Peters B, Ruttenberg A, Scheuermann RH, Brinkman RR, Courtot M, Mungall C, Xiang Z, Chen F, Todd T, Colby LA, Rush H, Whetzel T, Musen MA, Athey BD, Omenn GS, Smith B. Proceedings of the 1st International Conference on Biomedical Ontology (ICBO 2009), Buffalo, NY, USA. VO: Vaccine Ontology. The 1st International Conference on Biomedical Ontology (ICBO 2009), Buffalo, NY, USA. Nature Precedings. 2009. http://precedings.nature.com/documents/3553/version/1.
Lin Y, He Y. Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. Journal of Biomedical Semantics. 2012, 3:17. PMID: 23256535. PMCID: PMC3639077. (NOTE: This paper can be used for citing VO. We are currently preparing a journal article fully describing VO)
Ozgur A, Xiang Z, Radev D, He Y. Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. Journal of Biomedical Semantics. 2011, 2(Suppl 2):S8. PMID: 21624163. PMCID: PMC3102897. (Note: This paper may also be used for citing VO)

OAE: Ontology of Adverse Events

Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.

OVAE: Ontology of Vaccien Adverse Events

Marcos E , Zhao B, He Y. The ontology of vaccine adverse events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines. Journal of Biomedical Semantics. 2013 Nov 26;4(1):40. PMID: 24279920.

VICO: Vaccination Informed Consent Ontology:

Lin Y, Zheng J, He Y. VICO: Ontology-based representation and integrative analysis of vaccination informed consent forms. J Biomed Semantics. 2016 Apr 19;7:20. doi: 10.1186/s13326-016-0062-4. PMID: 27099700. PMCID: PMC4837519.

VIO: Vaccine Investigation Ontology:

Ong E, Sun P, Berke K, Zheng J, Wu G, He Y. VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. BMC Bioinformatics. 2019, 20(Suppl 21): 704. PMID: 31865910. PMCID: PMC6927110.

OGSF: Ontology of Genetic Susceptibility Factors, and its use in vaccine adverse event domain:

Lin Y, He Y. The Ontology of Genetic Susceptibility Factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. Journal of Biomedical Semantics. 2014, 5:19. doi:10.1186/2041-1480-5-19. PMID: 24963371. PMCID: PMC4068904.

INO: Interaction Network Ontology

Hur J, Özgür A, Xiang Z, He Y. Development and application of an Interaction Network Ontology for literature mining of vaccine-associated gene-gene interactions. Journal of Biomedical Semantics. 2015, 6:2. doi:10.1186/2041-1480-6-2. PMID: 25785184. PMCID: PMC4362819.

OBCS: Ontology of Biological and Clinical Statistics

Zheng J, Harris MR, Masci AM, Lin Y, Hero A, Smith B, He Y. The Ontology of Biological and Clinical Statistics (OBCS) for Standardized and Reproducible Statistical Analysis. J Biomed Semantics. 2016. Sep 14;7(1):53. PMID: 27627881. PMCID: PMC5024438.
Zheng J, Li H, Liu Q, He Y. The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. Quantitative Biology. 2017. 5(4):291-301.

Ontology-based Literature Mining:

Tiftikci M, Özgür A, He Y, Hur J. Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels. BMC Bioinformatics. 2019 20(Suppl 21):707. PMID: 31865904. PMCID: PMC6927101.
Hur J, Ozgur A, He Y. Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs. J Biomed Semantics. 2018. 9:17. PMID: 29880031. PMCID: PMC5991464
Hur J, Ozgur A, He Y. Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. J Biomed Semantics. 2017:12. DOI: 10.1186/s13326-017-0122-4. PMID: 28288685. PMCID: PMC5348867.
Hur J, Özgür A, He Y. The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. BioData Mining. 2016 Dec 19;9:41. PMID: 28031747. PMCID: PMC5168857.
Ozgur A, Hur J, Xiang Z, Ong E, Radev D, He Y. Ignet: A centrality and INO-based web system for analyzing and visualizing literature-mined networks. August 1-2, 2016, joint session ICBO+BioCreative, at the International Conference on Biomedical Ontologies (ICBO-2016) and BioCreative 2016, August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 2-page proceeding paper.
Karadeniz İ, Hur J*, He Y*, Ozgur A*. Literature mining and ontology based analysis of host-Brucella gene-gene interaction network. Front. Microbiol. 2015 Dec 9; 6:1386. PMID: 26696993. PMCID: PMC4673313.
Hur J, Özgür A, Xiang Z, He Y. Development and application of an Interaction Network Ontology for literature mining of vaccine-associated gene-gene interactions. Journal of Biomedical Semantics. 2015, 6:2. doi:10.1186/2041-1480-6-2. PMID: 25785184. PMCID: PMC4362819.
Y Zhang, C Tao, Y He, P Kanjamala, H Liu. Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. Journal of Biomedical Semantics 2013, 4:33 doi:10.1186/2041-1480-4-33. PMID: 24209834.
Xiang Z, Qin T, Qin Z, He Y. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks. BMC Systems Biology. 2013, 7(Suppl 3):S9. PMID: 24555475. PMCID: PMC3852244.
Hur J, Özgür A, Xiang Z, He Y. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. Journal of Biomedical Semantics. 2012, 3:18. PMID: 23256563. PMCID: PMC3599673.
Ozgur A, Xiang Z, Radev D, He Y. Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. Journal of Biomedical Semantics. 2011, 2(Suppl 2):S8. PMID: 21624163. PMCID: PMC3102897.
Hur J, Xiang Z, Feldman EL, He Y. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. BMC Immunology. 12(1):49 2011 Aug 26. PMID: 21871085.

Ontology-based modeling:

Lin Y, Xiang Z, and He Y. Ontology-based representation and analysis of host-Brucella interactions. J Biomed Semantics. 2015, 6:37. DOI: 10.1186/s13326-015-0036-y. PMID: 26445639. PMCID: PMC4594885.
Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone S, Soldatova LN, Stoeckert Jr. CJ, Turner J, Zheng J, the OBI consortium. Modeling biomedical experimental processes with OBI. Journal of Biomedical Semantics. 2010, 1(Suppl 1):S7. [PMID: 20626927]
Sarntivijai S, Zhang S, Jagannathan DG, Zaman S, Burkhart KK, Omenn GS, He Y, Athey BD, Abernethy DR. Linking MedDRA-coded clinical phenotypes to biological mechanisms by the Ontology of Adverse Events: A pilot study on Tyrosine Kinase Inhibitors (TKIs). Drug Safety. 2016. pp 1-11. First online: 22 March 2016. DOI: 10.1007/s40264-016-0414-0. PMID: 27003817. PMCID: PMC4933310.

Ontoanimal ontology tool development based on the VIOLIN R01 grant support:

Ontobee: http://www.ontobee.org:

Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y. Ontobee: A linked ontology data server to support ontology term
dereferencing, linkage, query, and integration. Nucleic Acid Research. 2017 Jan 4;45(D1):D347-D352. PMID: 27733503. PMCID: PMC5210626.
Xiang Z, Mungall C, Ruttenberg A, He Y. Ontobee: A Linked Data Server and Browser for Ontology Terms. Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO), Buffalo, NY, USA, July 28-30, 2011. Pages 279-281. [http://ceur-ws.org/Vol-833/paper48.pdf]

Ontofox: http://ontofox.hegroup.org:

Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: web-based support for ontology reuse. BMC Research Notes. 2010, 3:175. [PMID: 20569493]

Ontodog: http://ontodog.hegroup.org:

Zheng J, Xiang Z, Stoeckert Jr. CJ, He Y. Ontodog: a web-based ontology community view generation tool. Bioinformatics. 2014, 30(9):1340-2. doi: 10.1093/bioinformatics/btu008. [PDF] PMID: 24413522. PMCID: PMC3998133.

Ontorat: http://ontorat.hegroup.org:

Xiang Z, Zheng J, Lin Y, He Y. Ontorat: Automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. Journal of Biomedical Semantics. 2015, 6:4 doi:10.1186/2041-1480-6-4. PMID: 25785185. PMCID: PMC4362828.

Ontobull: http://ontobull.hegroup.org, and BFOConvert:

Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He. Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. August 1-2, 2016, joint session ICBO+BioCreative, at the International Conference on Biomedical Ontologies (ICBO-2016) and BioCreative 2016, August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 2-page proceeding paper (SOftware Demo).

Ontokiwi and Ontokiwi-based Ontobedia:

Ong E, He Y. Community-based ontology development, annotation and discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:65-74. eCollection 2016. PMID: 27570653. PMCID: PMC5001762.

Proposed eXtensible ontology development (XOD) principles:

He Y, Xiang Z, Zheng J, Lin Y, Overton JA, Ong E. The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. J Biomed Semantics. 2018 Jan 12;9(1):3. PMID: 29329592. PMCID: PMC5765662.

VO-based Annotation and Curation:

He Y, Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Res. 2010 Sep 27;6 Suppl 1:S5. [NAR] [PubMed] [PDF].
(Note: use VO to study Brucella vaccines)
Yang B, Sayers S, Xiang Z, He Y. Protegen: a web-based protective antigen database and analysis system. Nucleic Acids Research. 2010. 2010 Oct 19. [Epub ahead of print]. [PMID: 20959289]
(Note: all protective antigens in Protegen are annotated in VO)
Sayers S, Ulysse G, Xiang Z, and He Y. Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development. Journal of Biomedicine and Biotechnology. In press.
(Note: all vaccine adjuvants in Vaxjo are annotated in VO)

Vaccine adverse events:

Sarntivijai S, Xiang Z, Shedden KA, Markel H, Omenn GS, Athey BD, and He Y. Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines. PLoS ONE. 2012, 7(11): e49941. doi:10.1371/journal.pone.0049941.
Marcos E , He Y. The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing vaccine adverse events. Workshop “Vaccine and Drug Ontology Studies (VDOS 2013)". International Conference on Biomedical Ontologies (ICBO), Montreal, Qc, Canada. July 7, 2013 . Full-length proceeding paper. [http://ceur-ws.org/Vol-1061/Paper9_vdos2013.pdf]
Marcos E , Zhao B, He Y. The ontology of vaccine adverse events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines. Journal of Biomedical Semantics. 2013 Nov 26;4(1):40. PMID: 24279920.
Xie J, Zhao L, Zhou S, He Y. Statistical and ontological analysis of adverse events associated with monovalent and combination vaccines against hepatitis A and B diseases. Scientific Reports. 2016. 6:3418. PMID: 27694888. PMCID: PMC5046117.
Xie J, Codd C, Mo K, He Y. Differential adverse event profiles associated with BCG as a preventive tuberculosis vaccine or therapeutic bladder cancer vaccine identified by comparative ontology-based VAERS and literature meta-analysis. PLoS ONE. 2016 Oct 17;11(10):e0164792. PMID: 27749923. PMCID: PMC5066964.

Pathogen use case studies using VIOLIN or supported by the VIOLIN R01 funding:

COVID-19 vaccine use case:

Ong E, Wong M, Huffman A, He Y. COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning. Frontiers in Immunology. 11:1581. doi: 10.3389/fimmu.2020.01581. (Published: 03 July 2020.) PMID: 32719684. PMCID: PMC7350702.
Ong E, Huang X, Pearce R, Zhang Y, He Y. Computational Design of SARS-CoV-2 Spike Glycoproteins to Increase Immunogenicity by T Cell Epitope Engineering. Comput Struct Biotechnol J. 2021;19:518-529. doi: 10.1016/j.csbj.2020.12.039. Epub 2020 Dec 31. PMID: 33398234. PMCID: PMC7773544.

Brucella use case:

Xie J, Wang J, Li Z, Wang W, Pang Y, and He Y. Ontology-based meta-analysis of animal and human adverse events associated with licensed brucellosis vaccines. Frontiers in Pharmacology. 2018 May 15;9:503. PMID: 29867505. PMCID: PMC5962797.
He Y. Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics. Frontiers in Cellular and Infection Microbiology. 2012. 2:2. doi: 10.3389/fcimb.2012.00002.
He Y, Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Res. 2010 Sep 27;6 Suppl 1:S5. [NAR] [PubMed] [PDF].

Other use cases:

Wang Y, Wen Z, Pan X, Briles DE, He Y, Zhang JR. Novel immunoprotective proteins of Streptococcus pneumoniae identified by opsonophagocytosis killing screen. Infect Immun. 2018 Jun 11. pii: IAI.00423-18. PMID: 29891544.
Hur J, Ozgur A, He Y. Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. J Biomed Semantics. 2017:12. DOI: 10.1186/s13326-017-0122-4. PMID: 28288685. PMCID: PMC5348867.
Ni Z, Chen Y, Ong E, He Y. Antibiotic resistance determinants-focused Acinetobacter baumannii vaccine design using reverse vaccinology. International Journal of Molecular Sciences. 2017, 18(2), 458. PMID: 28230771. PMCID: PMC5343991.
Lopera-Madrid J, Osorio JE, He Y, Xiang Z, Adams LG, Laughlin RC, Mwangi W, Subramanya S, Neilan J, Brake D, Burrage TG, Brown WC, Clavijo A, Bounpheng MA. Safety and immunogenicity of mammalian cell derived and modified-vaccinia Ankara vectored African swine fever subunit antigens in swine. Veterinary Immunology and Immunopathology. 2017. DOI: 10.1016/j.vetimm.2017.01.004. PMID: 28241999.
McNamara L, He Y, Yang Z. Using epitope predictions to evaluate efficacy and population coverage of the Mtb72f vaccine for tuberculosis. BMC Immunology. 2010 Mar 30;11(1):18. [PMID: 20353587] [Journal Link]

Papers related to Community Participation:

Hur J, Tao C, He Y. A 2018 workshop: vaccine and drug ontology studies (VDOS 2018). BMC Bioinformatics. 2019 20(Suppl 21):705. PMID: 31865905. PMCID: PMC6927102.
Tao C, He Y, Arabandi S. Vaccine and Drug Ontology Studies (VDOS 2014). Journal of Biomedical Semantics..2016, 7:6. DOI: 10.1186/s13326-015-0039-8. PMID: 26918107.
Tao C, He Y, Arabandi S. A 2013 Workshop: Vaccine and Drug Ontology Studies (VDOS 2013). Journal of Biomedical Semantics. 2014 Mar 20;5(1):16. doi: 10.1186/2041-1480-5-16. PMID: 24650607. PMCID: PMC3994568. (Note: check: http://www2.unb.ca/csas/data/ws/semantic-trilogy-workshops/proceedings.html)
De Groot AS, De Groot P, He Y. ICoVax 2013: The 3rd ISV Pre-conference Computational Vaccinology Workshop. BMC Bioinformatics. 2014. In press. (Note: check: http://www.violinet.org/icovax2013)
He Y, Cao Z, De Groot AS, Brusic V, Schönbach C, Petrovsky N. Computational vaccinology and the ICoVax 2012 workshop. BMC Bioinformatics. 2013, 14(Suppl 4):I1 (8 March 2013). PMID: 23514034; PMCID: PMC3599086. (Note: check: http://www.violinet.org/icovax2012)
He Y, Toldo L, Burns G, Tao C, Abernethy DR. A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012). Journal of Biomedical Semantics 2012, 3:12. PMID: 23249650. PMCID: PMC3554582. (Note: check: http://kr-med.org/icbofois2012/vdosme/)
Note: The VDOS workshop sites can be found here: https://sites.google.com/site/vdosworkshop/system/app/pages/sitemap/hierarchy.

The OneNet Theory of Life and vaccine research:

He Y. Ontology-based vaccine and drug adverse event representation and theory-guided systematic causal network analysis towards integrative pharmacovigilance research. Current Pharmacology Reports. 2016, Volume 2, Issue 3, pp 113-128. DOI: 10.1007/s40495-016-0055-0.
He Y. Ontology-supported research on vaccine efficacy, safety, and integrative biological networks. Expert Reviews in Vaccines. 2014 Jul;13(7):825-41. doi: 10.1586/14760584.2014.923762. Epub 2014 Jun 7. PMID: 24909153. PMCID: PMC4815432.

Reviews and book chapters:

He Y. Genome-based computational vaccine discovery by reverse vaccinology (Chapter 5); in book: Immunomic Discovery of Adjuvants and Candidate Subunit Vaccines, edited by Darren R. Flower, Yvonne Perrie. Publisher: Springer, New York, 2013. ISBN-13: 978-1461450696. ISBN 978-1-4614-5070-2 (eBook). Links in: Google eBook, and Amazon book.
He Y, Xiang Z. Databases and in silico tools for vaccine design. Methods Mol Biol. 2013;993:115-27. doi: 10.1007/978-1-62703-342-8_8. PMID: 23568467. [Note: this is Chapter 8 in book: In Silico Models for Drug Discovery, Editor: Sandhya Kortagere.]
He Y. Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics. Frontiers in Cellular and Infection Microbiology. 2012. 2:2. doi: 10.3389/fcimb.2012.00002.

Special Feature Report on Dr. He and He group's vaccine informatics research by International Innovation:

Yongqun He: 'Analysing multidisciplinary vaccine mechanisms'. In research topic: The Mechanics of Health, International Innovation, July 2013, (Research Media, pp 41-43) ISSN 2041-4552.
(Note: International Innovation is the leading global dissemination resource for the wider scientific, technology and research communities, dedicated to disseminating the latest science, research and technological innovations on a global level. More information and a complimentary subscription offer to the publication can be found at: www.researchmedia.eu).

Notes: This website is not routinely updated and may miss some papers. More Hegroup publications can be found here: http://www.hegroup.org/publications.html (all areas).